package jalview.io;
+import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.ext.jmol.JmolParser;
import jalview.structure.StructureImportSettings;
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new FastaFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PfamFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
- return new StockholmFile();
+ return new StockholmFile(al);
}
},
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PIRFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new BLCFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
- return new BLCFile();
+ return new AMSAFile(al);
}
},
Html("HTML", "html", true, false)
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new HtmlFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new RnamlFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JSONFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PileUpfile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new MSFfile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new ClustalFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new PhylipFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return null; // todo is this called?
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new FeaturesFile();
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return new JmolParser(); // todo or null?
}
}
@Override
- public AlignmentFileI getAlignmentFile()
+ public AlignmentFileI getAlignmentFile(AlignmentI al)
{
return null;
}
return false;
}
- @Override
- public String getShortDescription()
- {
- return toString();
- }
-
/**
* Returns the file format with the given name, or null if format is null or
* invalid. Unlike valueOf(), this is not case-sensitive, to be kind to
{
return name;
}
+
+ @Override
+ public AlignmentFileI getAlignmentFile()
+ {
+ return getAlignmentFile((AlignmentI) null);
+ }
}